This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1d19

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1d19.gif|left|200px]]
+
{{Seed}}
 +
[[Image:1d19.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_1d19| PDB=1d19 | SCENE= }}
{{STRUCTURE_1d19| PDB=1d19 | SCENE= }}
-
'''SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT'''
+
===SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT===
-
==Overview==
+
<!--
-
The solution structures of two alternating purine-pyrimidine octamers, [d(G-T-A-C-G-T-A-C)]2 and the reverse sequence [d(C-A-T-G-C-A-T-G)]2, are investigated by using nuclear magnetic resonance spectroscopy and restrained molecular dynamics calculations. Chemical shift assignments are obtained for non-exchangeable protons by a combination of two-dimensional correlation and nuclear Overhauser enhancement (NOE) spectroscopy experiments. Distances between protons are estimated by extrapolating distances derived from time-dependent NOE measurements to zero mixing time. Approximate dihedral angles are determined within the deoxyribose ring from coupling constants observed in one and two-dimensional spectra. Sets of distance and dihedral determinations for each of the duplexes form the bases for structure determination. Molecular dynamics is then used to generate structures that satisfy the experimental restraints incorporated as effective potentials into the total energy. Separate runs start from classical A and B-form DNA and converge to essentially identical structures. To circumvent the problems of spin diffusion and differential motion associated with distance measurements within molecules, models are improved by NOE-based refinement in which observed NOE intensities are compared to those calculated using a full matrix analysis procedure. The refined structures generally have the global features of B-type DNA. Some, but not all, variations in dihedral angles and in the spatial relationships of adjacent base-pairs are observed to be in synchrony with the alternating purine-pyrimidine sequence.
+
The line below this paragraph, {{ABSTRACT_PUBMED_2231713}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 2231713 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_2231713}}
==About this Structure==
==About this Structure==
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D19 OCA].
+
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D19 OCA].
==Reference==
==Reference==
Line 25: Line 29:
[[Category: Double helix]]
[[Category: Double helix]]
[[Category: Nmr]]
[[Category: Nmr]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:20:07 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:02:27 2008''

Revision as of 19:02, 30 June 2008

Image:1d19.png

Template:STRUCTURE 1d19

SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT

Template:ABSTRACT PUBMED 2231713

About this Structure

Full experimental information is available from OCA.

Reference

Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement., Baleja JD, Germann MW, van de Sande JH, Sykes BD, J Mol Biol. 1990 Oct 5;215(3):411-28. PMID:2231713

Page seeded by OCA on Mon Jun 30 22:02:27 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1d19"
Personal tools